The loss snapped a 13-game winning streak for the Ducks, which was the longest in the nation coming into Saturday.
"It hurts and as I told them, you'd like to have some words that would take the pain out of it, but there aren't," Oregon coach Chip Kelly said. "We'll feel bad for a little bit of time and we'll bounce back from it."
Oregon's loss, coupled with No. 2 Kansas State's they were also the top two teams in the BCS standings means third-ranked Notre Dame is now the lone unbeaten team in the race for the BCS title game.
The Fighting Irish control their national championship run, with No. 4 Alabama and a couple of other Southeastern Conference teams also in the thick of it.
Oregon was the only Pac-12 team that Stanford hadn't defeated over the past two seasons. But the Cardinal's tough defense smothered the highest scoring team in the nation.
Alejandro Maldonado missed a 41-yard field goal for the Ducks to open overtime before Williamson's game winner.
Redshirt freshman Kevin Hogan threw for 211 yards and a game-tying fourth-quarter touchdown for Stanford, while Stepfan Taylor rushed for 161 yards on 33 carries.
UCLA 38, USC 28 • Brett Hundley passed for 234 yards and a touchdown and rushed for two more scores as No. 17 UCLA beat No. 21 USC in Pasadena, Calif., clinching the Pac-12 South title and emphatically snapping a five-game losing streak in their rivalry.
Eric Kendricks blocked a punt and made a fourth-quarter interception for the Bruins (9-2, 6-2 Pac-12), who overcame intermittent second-half rain and USC's star-studded lineup for a gutsy victory that puts them atop Los Angeles football.
Arizona State 46, Washington State 7 • Quarterbacks Taylor Kelly and Michael Eubank accounted for six touchdowns in Tempe, Ariz., and Arizona State became bowl eligible with a rout over Washington State that ended the Sun Devils' four-game losing streak.
Arizona State (6-5, 4-4 Pac-12) had failed in four tries to become bowl eligible, bogging down against some of the best teams in the conference.
Washington 38, Colorado 3 • Keith Price threw a career-best five touchdown passes and Washington overcame a slow start to whip hapless Colorado in Boulder, Colo., for the Huskies' fourth straight win.
Bishop Sankey atoned for a first-half fumble at the 1 by running through Colorado's defense for 139 yards and collecting 48 more on four receptions as the Huskies (7-4, 5-3 Pac-10) won consecutive road games for just the second time in the last decade.